tbuckley/cabot-search huggingface dataset:
Abstract 177: Ex vivo 3D culture of adenoid cystic carcinoma PDX models recapitulate disease biomarkers and predict drug response
Authors: Melissa Millard, Teresa M. DesRochers, Michael J. Wick, Jeffrey Kaufman, Nicole Spardy Burr
Journal: Cancer Research (2022)

Abstract Adenoid cystic carcinoma (ACC) is a rare, glandular cancer whose incidence rate and limited 2D cell culture capability make it difficult to study primary patient samples. Although well characterized ACC patient-derived xenografts (PDX) have proven to be a useful model to study disease mechanisms and therapeutic sensitives, animal drug studies are relatively low throughput, costly, and take months to accomplish. Ex vivo 3D cell culture can provide a high-throughput, less costly, and significantly faster platform for these drug studies but are hampered by the rarity of tissue. To address this unmet need for models of rare tumor types we developed 3D spheroid (3D-XPDXs™) and microtumor (3D-XPDXmt™) models of ACC using PDX as the primary tissue source. ACC PDX cells readily formed spheroids in our 3D-XPDXs™ platform, remained viable for up to 14 days, and maintained disease-relevant biomarkers such as MYB and c-kit. 3D-XPDXmt™ represent a more complex model of ACC by incorporating extracellular matrix. ACC 3D-XPDXmt™ displayed tumor-like morphologies concordant with the parental tumors and exhibited MYB and c-kit biomarker expression for up to 56 days in culture. Drug response profiling (DRP) was performed using the 3D-XPDXs™ ACC model with KIYATEC’s validated KIYA-PREDICT™ DRP platform. The screening panel consisted of drugs and drug-like compounds currently in use or under investigation for use in ACC, including broad-spectrum chemotherapies and targeted agents. Individualized drug responses were noted for each model as they exhibited differential sensitivities to DNA-damaging agents, microtubule stabilizers, and c-kit targeting kinase inhibitors mirroring the diversity of clinical outcomes. KIYA-PREDICT™ also identified drugs and drug-like compounds that uniformly inhibited viability. This is significant because there is currently no standard of care drugs for ACC, as few, if any have demonstrated homogenous responses in test populations. Monensin has been shown to inhibit activity of the MYB transcription factor, making it an attractive candidate drug for the treatment of ACCs which have a high prevalence of MYB activating alterations. In our study, monensin was effective in all three models with IC50 concentrations in the low micromolar range. These results correlate well with immunohistochemical staining of MYB in ACC 3D-XPDXs™ and 3D-XPDXmt™. Taken together, this data represents a new ex vivo 3D cell culture platform for the study of ACC biology and potential therapies. Citation Format: Melissa Millard, Teresa M. DesRochers, Michael J. Wick, Jeffrey Kaufman, Nicole Spardy Burr. Ex vivo 3D culture of adenoid cystic carcinoma PDX models recapitulate disease biomarkers and predict drug response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 177.
Abstract 3157: KLF5 defines the secretory lineage and governs sphingolipid metabolism in the skin
Authors: Yejing Ge
Journal: Cancer Research (2022)

Abstract Adult stem cells contribute to tissue regeneration and wound repair through cellular programs that can be hijacked by cancer cells. We previously reported such a phenomenon in skin, where squamous cell carcinomas adopt a plastic phenotype so called “stem cell lineage infidelity”, entailing a wide-spread co-expression of otherwise lineage restricted genes, exemplified by hair follicle factor SOX9 and interfollicular epidermal factor KLF5. Occurring transiently in wounds and persists in cancer, stem cell lineage infidelity is essential to drive wound repair and tumorigenesis. However, it remains unclear what were the functional mediators of lineage infidelity factors. We thus set out to investigate one of its defining factors, KLF5. Employing genome-wide transcriptome and epigenome profiling, we found KLF5 specifies the epidermal lineage in the skin and is essential for skin maturation in vivo. Strikingly, KLF5 binds to the genomic vicinity of, and transcriptionally controls, multiple key enzymes catalyzing rate-limiting steps of epidermal sphingolipid secretion, whose disruption led to loss of lipid ultrastructural integrity, compromised secretory machinery and selective decline of high complexity sphingolipids in the skin. Remarkably, lipid-rich dietary intervention was able to reverse skin defects caused by KLF5 ablation and KLF5 is prevalently disrupted in skin barrier and inflammatory diseases. Our findings suggest KLF5 serves as a master secretory lineage factor and a transcriptional governor of sphingolipid metabolism in the developing and diseased skin, warranting future investigation of its functional underpinning in wound repair and cancer. Citation Format: Yejing Ge. KLF5 defines the secretory lineage and governs sphingolipid metabolism in the skin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3157.
Abstract 2755: Transcriptomic changes experienced by activated and expanded NK cells for their use in the treatment of hematological malignancies
Authors: Chantal Reina-Ortiz, Pilar Mozas Alonso, Alberto Cebollada, David Ovelleiro, Luis Alberto Anel Bernal
Journal: Cancer Research (2022)

Abstract Natural Killer (NK) cells have shown great promise as a viable cell-based cancer immunotherapy. We have developed a protocol that produces expanded and highly activated NK (eNK) cells from healthy human donors that have been shown to be effective alone and in combination with monoclonal antibodies in a variety of hematological malignancies. The eNK cells showed a dramatic increase in cytolytic capacity after their expansion and activation using IL-2, IL-15, and 721.221 feeder cells. In order to elucidate the underlying mechanisms behind the changes, mRNAseq and miRNA arrays were performed on mRNA and miRNA samples, respectively, extracted from several NK expansions, taken at Day 0 (before activation) and Day 20 (after activation and expansion). Bioinformatic analysis was performed to identify differential gene expression changes and their downstream effects. Based on the genes with greatest differential expression, we quantified their corresponding proteins using flow cytometry, western blots, and ELISAs. Results reveal several discrete changes in the transcriptome that are reflected in changes in protein expression levels within the eNK cells. We conclude that the increased cytolytic capacity of eNK cells is due to the synergistic effect of variations in different genes responsible for target recognition, effector function, cell cycle progression and cell survival. These data can be used in the future to produce better eNK cells as treatment for hematological malignancies. Citation Format: Chantal Reina-Ortiz, Pilar Mozas Alonso, Alberto Cebollada, David Ovelleiro, Luis Alberto Anel Bernal. Transcriptomic changes experienced by activated and expanded NK cells for their use in the treatment of hematological malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2755.
Genomic Profiling and Response to Immune Checkpoint Inhibition plus Tyrosine Kinase Inhibition in FH-Deficient Renal Cell Carcinoma
Authors: Yunze Xu, Wen Kong, Ming Cao, Jieying Wang, Zaoyu Wang, Liang Zheng, Xiaoyu Wu, Rongrong Cheng, Wei He, Bo Yang, Baijun Dong, Jiahua Pan, Yonghui Chen, Jiwei Huang, Chen Jiang, Wei Zhai, Fangzhou Li, Ruohua Chen, Xiang Zhou, Guangyu Wu, Xiaochuan Geng, Jiasheng Chen, Huimin An, Yichu Yuan, Tianyuan Xu, Dongning Chen, Dengqiang Lin, Lieyu Xu, Kangbo Huang, Ling Peng, Yanfei Yu, Shengcheng Tai, Honggang Qi, Kai Luo, Xiaonan Kang, Hang Wang, Yiran Huang, Jin Zhang, Wei Xue
Journal: European Urology (2022)
Abstract 1503: Augmenting genomic instability in HPV head and neck cancer tumors through combination bromodomain and extra-terminal (BET) proteins inhibition and radiation treatments
Authors: Aakarsha Rao, Zijian Ni, Albert Wang, Dhruthi Suresh, Chitrasen Mohanty, Christina Kendziorski, Gopal Iyer
Journal: Cancer Research (2022)

Abstract Integration of human papillomavirus (HPV)16 genomes into host head and neck squamous cell carcinoma (HNSCC) DNA is an essential driver for cancer progression. Currently, there are no treatment strategies based on HPV integration status. We postulate that a conceptual advance in the treatment of HPV HNSCC cancer can be formalized by targeting transcriptional co-regulator - bromodomain and extra-terminal (BET) proteins which mediate viral and host transcription. HPV maintenance in the host environment is dependent on BET protein-BRD4. An additional function of BET proteins in regulating transcription of tumor suppressors and DNA damage repair (DDR) genes. Given that patient populations have viral integrations into their genomes and its maintenance depends on cellular Brd4, displacing Brd4 through novel second-generation BET inhibitors can abrogate HPV transcription. Through chemical and knockdown studies of BET proteins in integrated viral HNSCC cells, we show viral oncogenes E6 and E7 are directly regulated by Brd4, reactivate tumor suppressors p53, release E2F1-Rb cell cycle brake to induce G1 cell cycle arrest, and significantly converge towards downregulation of DDR pathways in disrupted viral genomes. In contrast, non-disrupted viral genomes diverge from DDR pathways towards downregulation of interferon signaling pathways. As a result of the intrinsic genomic instability caused by the downregulation of components of the DDR machinery, the addition of external beam radiation further delayed DNA repair kinetics quantified through H2AX foci formation in cells harboring disrupted viral genomes. Taken together, targeting BET proteins is not a viable monotherapy but creates genomic instability, which, when combined with radiation, has the potential to eradicate HPV-associated tumors. Citation Format: Aakarsha Rao, Zijian Ni, Albert Wang, Dhruthi Suresh, Chitrasen Mohanty, Christina Kendziorski, Gopal Iyer. Augmenting genomic instability in HPV head and neck cancer tumors through combination bromodomain and extra-terminal (BET) proteins inhibition and radiation treatments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1503.
Abstract 1162: A systematic analysis of RET mutations and their sensitivity to different RET inhibitors
Authors: Shay Rotkopf, DIkla Haham, Natalie Fillipov-Levy, Lea Birnbaum, Elinor Dehan, Ilona Kifer, Zohar Barbash, Gabi Tarcic
Journal: Cancer Research (2022)

Abstract The RET oncogene is a receptor tyrosine kinase, mainly expressed in neural crest-derived tissues, that plays a role in cell growth and differentiation. Since the first identification of inherited mutations in RET as the cause of Multiple endocrine neoplasia type 2 (MEN2), somatic RET alterations have been identified as actionable drivers in subtypes of lung and thyroid, among other cancer types. This enabled the development of several RET targeted treatments, such as pralsetinib and selpercatinib, showing meaningful clinical benefit. To understand the full scope of RET alteration frequency and heterogeneity we used the AACR-GENIE database. We found that the frequency of RET alterations pan-cancer is 3%, of which two-thirds are missense mutations. The major cancer types with RET alterations are medullary thyroid, papillary thyroid and NSCLC, as expected, but also breast, colorectal and melanoma. An important distinction between NSCLC and thyroid cancer compared to colorectal, breast and melanoma is the fraction of missense vs. fusion events, with 30%-40% of samples in the former group containing RET fusions. This is in contrast with &amp;gt;80% of samples in the latter group containing RET missense mutations. Moreover, the heterogeneity of RET alterations is large, with over 1,000 unique types of missense mutations identified. The vast majority of mutations are classified as variants of uncertain significance (VUS). To better understand the potential activity of these mutations, we assayed over 200 different missense mutations and fusions using a high-throughput cell-based functional assay. Results were analyzed using a novel machine learning model consisting of a multi-scale deep convolutional neural net, followed by a tree-based regressor. Our results show that the assay correctly predicted the activity of both known activating alterations as well as of loss of function mutations. Interestingly, only ~3% of over 150 VUS tested were found to be activating. Furthermore, we show that the active alterations are sensitive to the FDA-approved targeted agents pralsetinib and selpercatinib, with varying IC50 values. Taken together, these results uncover the full extent of actionable RET alterations, differentiating between active and non-active variants, as well as the effectiveness of RET inhibitors. Citation Format: Shay Rotkopf, DIkla Haham, Natalie Fillipov-Levy, Lea Birnbaum, Elinor Dehan, Ilona Kifer, Zohar Barbash, Gabi Tarcic. A systematic analysis of RET mutations and their sensitivity to different RET inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1162.
Abstract 6061: Novel β-Apopicropodophyllin derivative, JNC-1043, exerts anti-cancer and radiosensitizing effects
Authors: Jong Kuk Park, A-Ram Kang, Jin-Hee Kwon, Jong-Ryoo Choi, Jie-Young Song, Sang-Gu Hwang
Journal: Cancer Research (2022)

Abstract In this study, we reported novel anti-cancer drug candidate, JNC-1043{(5S)-5-(4-Benzyloxy-3,5-dimethoxy-phenyl)-5,9-dihydro-8H-furo[3',4':6,7] naphtho[2,3-d][1,3]dioxol-6-one}, synthesized from β-Apopicropodophyllin. Firstly, we analyzed anti-cancer effect of JNC-1043. We performed MTT assay to detect IC50 values on several cancer cells - breast, lung, pancreatic, blood, gastric, colorectal cancers. In these experiments, 0.1~1 μM IC50 values of JNC-1043 were calculated, and JNC-1043 treatments induced activation of caspase-3 and -8. Additionally, effective values of pharmacokinetic parameters in male rats and 2 weeks Dose Rate Finding (DRF) of JNC-1043 also detected. This result showed JNC-1043 is a promising anti-cancer candidate. Next, we tested whether radiosensitizing effect of JNC-1043. Each IC50 values of DLD-1 and HCT116 cell lines were calculated as 0.157, 0.1145, respectively. Cell counting assays were performed and then showed combination of JNC-1043 and γ-ionizing radiation (IR) enhanced cell death. JNC-1043 only- or IR only-treatment induced cell death by 50~60%, respectively, while combination of JNC-1043 and IR increased more 20~30% cell death than those of JNC-1043 only- or IR only-treatment in both cell lines. Clonogenic assay also performed, and then dose enhancement ratios (DER) of DLD-1 and HCT116 were calculated as 1.40, 1.53, respectively. Apoptosis also was detected with Annexin V-Propidium iodide assay. Combination of JNC-1043 and IR increased apoptosis more 30~40% than those of JNC-1043 only- or IR only-treatment. DCFDA-based assay also were performed to indicate ROS production was enhanced in combination of JNC-1043 and IR. In vivo xenograft experiment, combination of JNC-1043 and IR reduced tumor sizes less 50% and increased apoptosis more 30~40% than those of JNC-1043 only- or IR only-treatment. These results implied anti-cancer and radiosensitizing effect of JNC-1043 resulted from promotion of apoptosis via enhancement of ROS production. Citation Format: Jong Kuk Park, A-Ram Kang, Jin-Hee Kwon, Jong-Ryoo Choi, Jie-Young Song, Sang-Gu Hwang. Novel β-Apopicropodophyllin derivative, JNC-1043, exerts anti-cancer and radiosensitizing effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6061.
Abstract 1954: Circulating tumor cell kinetics and rare cell morphology monitor disease progression in patients with metastatic colorectal cancer
Authors: Sachin Narayan
Journal: Cancer Research (2022)

Abstract As the world’s third most common cancer and second leading cause of oncology-related deaths, colorectal cancer (CRC) poses a variety of clinical challenges. CRC is marked by its extensive solid tumor heterogeneity and the difficulties in longitudinally monitoring a patient’s disease status. Being a minimally invasive prognostic tool, the liquid biopsy has immense potential to improve current clinical practice by providing real-time personalized information over the course of treatment. Utilizing the High-Definition Single Cell Assay (HDSCA) workflow, we employed a “no cell left behind approach” to analyze peripheral blood samples from metastatic CRC (mCRC) patients at various timepoints during treatment. We highlight the circulating rare cell population present in the liquid biopsy of mCRC patients, showing the spatial and temporal heterogeneities of CTCs. We observed a significant association between CTC subcategorization based on morphological differences and survival, emphasizing the heterogeneity within the CTC classification. Moreover, considering the time of sample collection in relation to the clinical scenario is critical in determining the prognostic relevance of static cellular enumerations as well as the change in cell populations over time. Through the integration of cellular morphology in a time-based analysis, the liquid biopsy can provide insight into the pathophysiology of mCRC by highlighting the complexity of the disease to monitor treatment response. Citation Format: Sachin Narayan. Circulating tumor cell kinetics and rare cell morphology monitor disease progression in patients with metastatic colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1954.
Abstract 1600: Dose-dependent effects of interferon-gamma treatment on pancreatic ductal adenocarcinoma cell states
Authors: Deborah A. Liberman, Dalia Barkley, Itai Yanai
Journal: Cancer Research (2022)

Abstract Interferon-gamma (IFNγ) is a canonical proinflammatory cytokine that has well-studied antitumor functions such as the upregulation of MHC Class I (MHC-I), increased Th1 development, macrophage activity, innate immune cell recruitment, and in tumor cells increased apoptosis, decreased angiogenesis and proliferation. However, IFNγ is also important in limiting tissue destruction due to inflammation, taking on an immunotolerant role and allowing cancer cells to evade immune surveillance. We previously identified an interferon response cell state across diverse cancer types, as defined by the relative expression of IFIT1, HLA-A, HLA-DRA, STAT1, and IRF1. The interferon response cell state is heterogeneously expressed in cancer cells and appears to function both by cancer cell extrinsic and intrinsic mechanisms. Several clinical trials have tested the efficacy of IFNγ as a therapeutic for immune system stimulation in patients with melanoma. However, these have failed to detect effective outcomes, and have even noted some pro-growth actions, perhaps consistent with IFNγ’s immunotolerant role in maintaining tissue homeostasis. We are interested in identifying cell populations that are vulnerable to the antitumor functions of IFNγ, as well as cell populations that may be susceptible to IFNγ’s pro-tumor actions. To test this, we treated a pancreatic ductal adenocarcinoma cell line with three doses of IFNγ in vitro every day for five days and analyzed expression of proteins associated with IFNγ signaling by flow cytometry each day. Distinct doses of IFNγ have been shown to affect varying degrees of antitumor and pro-tumor responses. For example, growth inhibition has been seen upon treatment with high dose IFNγ, while treatment with low dose IFNγ is consistent with increased metastatic capability such as increased resistance to cytotoxic lymphocytes and natural killer cells despite the upregulation of MHC-I. We thus treated cells with three doses of IFNγ: low, normal, and high. Preliminary results have shown a dose dependent effect of IFNγ including the upregulation of MHC-I and PDL1. Ongoing work includes identifying changes in cell states using single-cell RNA-sequencing to uncover how cancer cells respond to varying intensities of IFNγ exposure. Additionally, we are analyzing how release of IFNγ from cancer cells changes following treatment of IFNγ at different doses. This work will provide insight into the mechanisms by which cancer cells evade immune surveillance and how cell states can describe a tumor’s vulnerability to IFNγ’s antitumor and pro-tumor effects. Citation Format: Deborah A. Liberman, Dalia Barkley, Itai Yanai. Dose-dependent effects of interferon-gamma treatment on pancreatic ductal adenocarcinoma cell states [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1600.